SNP Detail Info-rs2117266

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

NBEAL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0429 (12823/29884,GnomAD)
G==0414 (12059/29118,TOPMED)
G==0492 (2465/5008,1000G)
G==0305 (1176/3854,ALSPAC)
G==0316 (1170/3708,TWINSUK)

Position: chr2:203195425 (GRCh38.p7) (2q33.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 17 Enhancers around

Promoter: 28 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.203195425G>T
GRCh37.p13 chr 2	NC_000002.11:g.204060148G>T

Molecule type	Change	Amino acid[Codon]	SO Term
NBEAL1 transcript	NM_001114132.1:c.	N/A	Intron Variant
NBEAL1 transcript variant X5	XM_005246787.3:c.	N/A	Intron Variant
NBEAL1 transcript variant X9	XM_005246788.2:c.	N/A	Intron Variant
NBEAL1 transcript variant X1	XM_006712698.3:c.	N/A	Intron Variant
NBEAL1 transcript variant X4	XM_006712699.3:c.	N/A	Intron Variant
NBEAL1 transcript variant X2	XM_011511658.2:c.	N/A	Intron Variant
NBEAL1 transcript variant X3	XM_011511659.2:c.	N/A	Intron Variant
NBEAL1 transcript variant X6	XM_011511660.2:c.	N/A	Intron Variant
NBEAL1 transcript variant X7	XM_011511662.2:c.	N/A	Intron Variant
NBEAL1 transcript variant X9	XM_017004728.1:c.	N/A	Intron Variant
NBEAL1 transcript variant X10	XM_017004729.1:c.	N/A	Intron Variant
NBEAL1 transcript variant X8	XM_011511663.2:c.	N/A	Genic Downstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.616	T=0.384
1000Genomes	American	Sub	694	G=0.450	T=0.550
1000Genomes	East Asian	Sub	1008	G=0.659	T=0.341
1000Genomes	Europe	Sub	1006	G=0.315	T=0.685
1000Genomes	Global	Study-wide	5008	G=0.492	T=0.508
1000Genomes	South Asian	Sub	978	G=0.360	T=0.640
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.305	T=0.695
The Genome Aggregation Database	African	Sub	8698	G=0.558	T=0.442
The Genome Aggregation Database	American	Sub	834	G=0.420	T=0.580
The Genome Aggregation Database	East Asian	Sub	1608	G=0.676	T=0.324
The Genome Aggregation Database	Europe	Sub	18442	G=0.350	T=0.649
The Genome Aggregation Database	Global	Study-wide	29884	G=0.429	T=0.570
The Genome Aggregation Database	Other	Sub	302	G=0.190	T=0.810
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.414	T=0.585
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.316	T=0.684

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs2117266	0.00016	alcohol dependence(early age of onset)	20201924
rs2117266	0.00093	alcohol dependence	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:204060148	ICA1L	ENSG00000163596.12	G>T	3.1624e-3	323440	Caudate_basal_ganglia

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	204105281	204105453	E068	45133
chr2	204106087	204106127	E068	45939
chr2	204106167	204106226	E068	46019
chr2	204102436	204102532	E069	42288
chr2	204105281	204105453	E069	45133
chr2	204105281	204105453	E070	45133
chr2	204102436	204102532	E071	42288
chr2	204105281	204105453	E071	45133
chr2	204106087	204106127	E071	45939
chr2	204106167	204106226	E071	46019
chr2	204102436	204102532	E072	42288
chr2	204105281	204105453	E073	45133
chr2	204102436	204102532	E074	42288
chr2	204105281	204105453	E074	45133
chr2	204105281	204105453	E081	45133
chr2	204102436	204102532	E082	42288
chr2	204105281	204105453	E082	45133

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	204103046	204103116	E067	42898
chr2	204103208	204104703	E067	43060
chr2	204104773	204104956	E067	44625
chr2	204103046	204103116	E068	42898
chr2	204103208	204104703	E068	43060
chr2	204104773	204104956	E068	44625
chr2	204103046	204103116	E069	42898
chr2	204103208	204104703	E069	43060
chr2	204104773	204104956	E069	44625
chr2	204103046	204103116	E070	42898
chr2	204103208	204104703	E070	43060
chr2	204104773	204104956	E070	44625
chr2	204103046	204103116	E071	42898
chr2	204103208	204104703	E071	43060
chr2	204104773	204104956	E071	44625
chr2	204103046	204103116	E072	42898
chr2	204103208	204104703	E072	43060
chr2	204104773	204104956	E072	44625
chr2	204103046	204103116	E073	42898
chr2	204103208	204104703	E073	43060
chr2	204104773	204104956	E073	44625
chr2	204103046	204103116	E074	42898
chr2	204103208	204104703	E074	43060
chr2	204104773	204104956	E074	44625
chr2	204103208	204104703	E081	43060
chr2	204103046	204103116	E082	42898
chr2	204103208	204104703	E082	43060
chr2	204104773	204104956	E082	44625

rs2117266